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Issue #123: Add anib#338

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baileythegreen wants to merge 81 commits intomasterwiddowquinn/pyani:masterfrom anib_123widdowquinn/pyani:anib_123Copy head branch name to clipboard

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Commits on Jul 15, 2021

• Initial split of v2 ANIb code into anib.py and aniblastall.py files

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Commits on Jul 21, 2021

• Updated comments/logging

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• Added sysexit when adding genomes to the database fails

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• Added initial versions of functions and comments about needed code

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• Rename fraglens to fragsizes for consistency with anib.py

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Commits on Sep 13, 2021

• Add add_blastdb() to pyani_orm.py

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• Change default for maxmatch from None to False

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• Add/expand code to process input genomes

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• Split genome files into contiguous fragments

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• Implement generate_joblist()

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• Implement run_anib_jobs()

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• Implement update_comparisons_results() and commit to database

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• Update call to generate_joblist()

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• Update name of output file in fragment_fasta_file()

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• Update value passed for maxmatch to a boolean

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• Implement remainder of subcmd_anib()

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• Add a commented question

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• Alter generate_blastn_commands() to only take one query/subject pair

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• Alter construct_blastn_cmdline() for a single query/subject pair

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• Remove method parameter from process_blast() call

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• Change outfilename in `construct_makeblastdb_cmd()

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• Move aniblastall-specific tests to test_aniblastall.py

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• Change call to parse_blast_tab() to not use method parameter

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• Skip tests as a result of changes to how command lines are generated

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• Add get_version() tests and boilerplate

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• Merge branch 'master' of https://github.com/widdowquinn/pyani into anib_123

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Commits on Sep 14, 2021

• Make changes to reflect splitting of anib and aniblastall

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Commits on Sep 21, 2021

• Add tests for get_version()

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Commits on Sep 22, 2021

• Fixed typos and put one variable name in camelcase

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• Fix which file is passed as input and which as blastdb

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• Move serialisation of fragment dictionary to primary function

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• Added useful debugging lines to anib.py

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• Add long versions of CLI flags to anib_parser.py

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• Comment out (likely) unnecessary function

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• Update docstrings to reflect new comparison handling

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• Add useful debugging lines

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• Populate aniblastall_parser.py

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• Comment out (likely) unnecessary function

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• Simplify generation of command lines and update supporting docstrings

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• Update command name referenced in docstrings

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• Fix which files are passed as input and blastdb in command generation

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• Add useful debugging lines

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• Add imports and convenience struct for ComparisonJob

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• Add initial code for starting a run and adding it to the database

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• Add genomes for the ru to the database

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• Get genomes for the run and create output directories

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• Add code to fragment fasta files

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• Add code to create blastdb

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• Add code to generate list of comparisons and filter existing ones

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• Add code for case where all comparisons have been run already

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• Add code for recovery mode

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• Rename blastcmd to blastallcmd

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• Add generate_joblist()

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• Add code to generate joblist

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• Add code to run comparisons

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• Add code to update database

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• Remove or rename things specific to anib to aniblastall

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• Skip unnecessary tests

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• Add dir_aniblastall_in() fixture

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Commits on Sep 30, 2021

• Add lines debugging

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Commits on Oct 5, 2021

• Fix naming of elements in `test_subcmd_anib" namespace

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• Update naming of TestANIbSubcommand()

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• Switch to use NamedTuple

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• Add test_subcmd_10_aniblastall.py

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• Make test_subcmd_04_anim.py match other method subcommand tests

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• Fix names of executable variables

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Commits on Oct 7, 2021

• Pass both stdout and stderr to the regex version search

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• Set indir and outdir to required in anib_parser.py

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• Add docs/subcmd_anib.rst

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• Add documentation for aniblastall

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Commits on Dec 12, 2021

• Merge branch 'master' of https://github.com/widdowquinn/pyani into anib_123

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• Replace f-strings in logging statements

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Commits on Apr 13, 2022

• Update .gitignore

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• Merge branch 'master' of https://github.com/widdowquinn/pyani into anib_123

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• Update call to add_run() to fit the function's new return value

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• Remove f-strings from logging calls

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Commits on May 11, 2022

• Merge branch 'master' of https://github.com/widdowquinn/pyani into anib_123

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Commits on May 16, 2022

• Merge branch 'master' of https://github.com/widdowquinn/pyani into anib_123

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Commits on Jun 7, 2022

• update deprecated behaviours in pandas

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• remove unused import

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Commits on Jun 16, 2022

• Merge branch 'master' of https://github.com/widdowquinn/pyani into anib_123

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